Structure and dynamics of a (1:1) drug-DNA complex: Analysis of 2D NMR data using molecular mechanics and molecular dynamics calculations

Conference · Mon Jan 01 00:00:00 EST 1990

DOI:https://doi.org/10.1007/978-94-011-3728-7_6· OSTI ID:6941313

Sarma, R H; Sarma, M H; Umemoto, K ^[1]; Gupta, G; Garcia, A E ^[2]

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1. State Univ. of New York, Albany, NY (USA). Dept. of Chemistry
2. Los Alamos National Lab., NM (USA)

1D/2D NMR studies are reported for a (1:1) complex of d(GA{sub 4}T{sub 4}C){sub 2} and Dst2 (an analogue of distamycin A). Full- Matrix NOESY Simulations, Molecular Mechanics and Molecular Dynamics Calculations are performed to analyze the NMR data. Results show that drug-DNA complex formation is driven by static features like H-bonding and steric interactions in the minor-groove of DNA. As a consequence of drug binding, a non-linear oscillatory mode is activated. In this mode the molecule samples equilibrium structural states of difference degrees of bending. It is noted that these structures belong to three distinctly different energy wells that satisfy the same NMR data. 14 refs., 4 figs., 2 tabs.

• Research Organization: Los Alamos National Laboratory (LANL), Los Alamos, NM (United States)
• Sponsoring Organization: DOE/MA; NIOSH; National Science Foundation (NSF)
• DOE Contract Number: W-7405-ENG-36
• OSTI ID: 6941313
• Report Number(s): LA-UR-90-1604; CONF-9005204-1; ON: DE90011977; CNN: C-670; PR0095; TRN: 90-018546
• Resource Relation: Journal Volume: 23; Conference: 23. Jerusalem symposium on molecular basis of specificity in nucleic acid-drug interactions, Jerusalem (Israel), 7-11 May 1990
• Country of Publication: United States
• Language: English

Related Subjects

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75 CONDENSED MATTER PHYSICS
SUPERCONDUCTIVITY AND SUPERFLUIDITY
DNA
MOLECULAR STRUCTURE
DRUGS
CHEMICAL BONDS
CHEMICAL SHIFT
INTERATOMIC DISTANCES
NUCLEAR MAGNETIC RESONANCE
DISTANCE
MAGNETIC RESONANCE
NUCLEIC ACIDS
ORGANIC COMPOUNDS
RESONANCE
550200* - Biochemistry
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